Contacts of the strand formed by residues 37 - 43 (chain D) in PDB entry 3F5O
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with LYS 37 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32D SER* 4.1 1.4 + - - +
33D ALA* 3.7 1.4 - - - -
34D ALA* 2.9 39.8 + - + +
35D PRO 3.2 4.7 + - - +
36D GLY* 1.3 80.4 - - - +
38D VAL* 1.3 68.2 + - - +
39D ILE* 3.8 22.1 - - + +
71D ALA* 4.3 2.0 + - - +
103D THR* 3.8 19.4 - - + +
104D ALA 3.3 11.2 - - - +
105D HIS* 3.4 32.6 + - + +
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Residues in contact with VAL 38 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8D LEU* 3.9 17.5 - - + -
30D LEU* 3.9 22.2 - - + -
32D SER 3.5 4.7 - - - +
33D ALA* 4.6 0.9 - - - -
37D LYS* 1.3 78.6 - - - +
39D ILE* 1.3 66.5 + - - +
40D CYS* 3.9 7.9 - - - -
67D ILE* 3.8 27.1 - - + +
70D MET* 3.8 11.4 - - + +
71D ALA* 3.6 28.2 - - + +
74D CYS* 4.1 7.6 - - - -
102D ILE 3.6 1.0 - - - +
103D THR* 3.5 2.6 - - - +
104D ALA* 2.8 37.4 + - - +
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Residues in contact with ILE 39 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30D LEU* 3.4 5.9 - - - +
31D VAL* 2.8 49.0 + - + -
32D SER* 3.0 30.8 + - - +
37D LYS* 3.8 33.4 - - + +
38D VAL* 1.3 77.6 - - - +
40D CYS* 1.3 58.9 + - - +
41D GLU* 5.4 0.2 - - - +
101D VAL* 3.7 28.3 - - + -
102D ILE 3.4 2.5 - - - +
103D THR* 4.0 12.6 - - + +
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Residues in contact with CYS 40 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12D ILE* 4.2 7.4 - - - -
28D ILE* 3.9 27.6 - - + -
29D THR 3.1 13.9 - - - +
30D LEU* 3.9 16.8 - - - -
31D VAL* 4.2 0.7 - - - +
38D VAL* 3.9 11.2 - - - -
39D ILE* 1.3 78.7 - - - +
41D GLU* 1.3 70.4 + - - +
67D ILE* 4.0 15.0 - - + -
70D MET* 4.5 0.7 - - - -
101D VAL* 3.5 2.8 - - - +
102D ILE* 2.8 42.7 + - + +
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Residues in contact with GLU 41 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27D LYS 4.5 0.2 - - - +
28D ILE* 3.3 4.7 - - - +
29D THR* 2.8 46.0 + - - +
31D VAL* 3.6 24.0 - - + +
39D ILE* 5.4 0.3 - - - +
40D CYS* 1.3 80.2 - - - +
42D MET* 1.3 62.5 + - - +
99D ASP* 6.3 1.1 - - + -
100D ILE 3.2 13.7 - - - +
101D VAL* 4.0 15.5 - - + +
102D ILE* 4.2 3.1 - - - -
123D LYS* 2.9 45.4 + - + +
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Residues in contact with MET 42 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25D LEU* 5.1 3.8 - - - -
27D LYS* 4.3 8.7 - - + -
28D ILE* 3.8 32.5 - - + +
29D THR* 6.2 0.2 - - - -
41D GLU* 1.3 77.7 - - - +
43D LYS* 1.3 69.9 + - - +
44D VAL* 3.9 5.1 + - + -
48D HIS* 3.7 43.1 - - + +
55D LEU* 4.1 15.9 - - + -
59D LEU* 4.3 2.7 - - + -
63D LEU* 4.2 14.1 - - + -
99D ASP* 3.6 2.6 - - - -
100D ILE* 2.8 60.3 + - + +
102D ILE* 4.1 3.6 - - + +
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Residues in contact with LYS 43 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27D LYS* 5.0 4.2 + - - +
42D MET* 1.3 76.3 - - - +
44D VAL* 1.3 73.3 + - - +
45D GLU* 3.2 23.2 + - + +
48D HIS* 3.5 16.5 - - - -
97D GLY* 3.2 29.1 + - - +
98D GLU 3.5 7.2 - - - +
99D ASP* 3.2 31.3 + - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il